Supplementary online material to V. Bourret et al.’s « Whole-genome, deep pyrosequencing analysis of a duck influenza A virus evolution in swine cells »
Table S1. PCR conditions specific for each segment. See main text for remaining PCR conditions (identical across segments) and details about the different HA primers used. Non subtype-specific HA primers bear restriction sites at their 5' end for use in cloning. We needed subtype-specific PCR primers for segment 4 only as the H1 and H11 alleles each comprised nearly 50% of the population and were so divergent that mixed chromatograms were unreadable. In the case of other segments, the different alleles would be much less divergent, resulting in easily readable mixed chromatograms (see for instance figure 1).
Table S2. Internal primers used for the sequencing of full-length genomes of the parental A/mallard/Netherlands/10/99 stock and its NPTr-adapted descendent. *, anti-sense primer.
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School of Biological Sciences, University of Manchester, Manchester, UK. Running title: Detection and quantification of positively selected sites in HIV.
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